In defeating the interim government and its army, the RPF ended the genocide. At the same time, its troops committed grave violations of international humanitarian law by attacking and killing unarmed civilians. Unlike the genocidal authorities who undertook a complex campaign involving all the machinery of the state and aiming to involve all Hutu citizens, the RPF ran a straightforward military campaign where civilians generally provided only information or support services.

The RPF permitted its soldiers to kill persons whom they took to be Interahamwe or other supposed participants in the genocide. They killed some in the course of their military advance, but they executed most in the days and weeks after combat had finished. They selected the victims from among civilians grouped in camps, sometimes relying on accusations by survivors, sometimes on their own interrogations. They executed some persons apparently because they were linkedwith parties opposed to the RPF or showed potential for becoming political leaders rather than because they were thought guilty of involvement in the genocide.

In a number of places, such as in the communes of Ntyazo, Mukingi and Runda, RPF soldiers massacred unarmed civilians, many of them women and children, who had assembled for a meeting on their orders. The people were told to come to receive food or to be given instructions or to gather before being transported to another site. The RPF soldiers also massacred several hundred people in the Byumba stadium in mid-April.

In a series of raids in Kigali in early April, RPF soldiers killed dozens of political and military leaders, many of them past government employees or persons close to Habyarimanas political party. They killed family members, including women and children, in a number of these cases.

The RPF was commonly acknowledged by military experts to be a highly disciplined force, with clear lines of command and adequate communication. Although it may have become less disciplined during the months of the genocide due to the incorporation of new recruits, RPF commanding officers like General Paul Kagame maintained the authority necessary to ensure compliance with their orders. The crimes committed by RPF soldiers were so systematic and widespread and took place over so long a period of time that commanding officers must have been aware of them. Even if they did not specifically order these practices, in most cases they did not halt them and punish those responsible.

In early November 1994, the RPF reported that it had arrested twenty-five soldiers for capital crimes, eight of them accused of killing civilians between June and August 1994 and by the end of the year military prosecutors had supposedly completed investigations in some twenty such cases. One major, one corporal and four soldiers indicted for these crimes were tried and convicted in 1997 and 1998. The major was sentenced to life in prison and the others to imprisonment for terms ranging from two to five years.

After some early but limited reports of killings by the RPF, the first substantial charges against RPF forces were made by Robert Gersony, a consultant to the U.N. High Commissioner for Refugees. After interviewing hundreds of Rwandans inside and outside the country in July and August 1994, he concluded that the RPF had engaged in widespread and systematic slaughter of unarmed civilians. In September 1994, the U.N., in agreement with the U.S. and perhaps others, agreed to suppress the report but demanded that the RPF halt the killings. The number of killings declined markedly after September in the face of this international pressure.